The effect of fibre cell remodelling on the power and optical quality of the lens.

Vertebrate eye lenses are uniquely adapted to form a refractive index gradient (GRIN) for improved acuity, and to grow slowly in size despite constant cell proliferation. The mechanisms behind these adaptations remain poorly understood. We hypothesize that cell compaction contributes to both. To test this notion, we examined the relationship between lens size and shape, refractive characteristics and the cross-sectional areas of constituent fibre cells in mice of different ages. We developed a block-face imaging method to visualize cellular cross sections and found that the cross-sectional areas of fibre cells rose and then decreased over time, with the most significant reduction occurring in denucleating cells in the adult lens cortex, followed by cells in the embryonic nucleus. These findings help reconcile differences between the predictions of lens growth models and empirical data. Biomechanical simulations suggested that compressive forces generated from continuous deposition of fibre cells could contribute to cellular compaction. However, optical measurements revealed that the GRIN did not mirror the pattern of cellular compaction, implying that compaction alone cannot account for GRIN formation and that additional mechanisms are likely to be involved

Prediction of protein binding sites in protein structures using hidden Markov support vector machine

<p>Abstract</p> <p>Background</p> <p>Predicting the binding sites between two interacting proteins provides important clues to the function of a protein. Recent research on protein binding site prediction has been mainly based on widely known machine learning techniques, such as artificial neural networks, support vector machines, conditional random field, etc. However, the prediction performance is still too low to be used in practice. It is necessary to explore new algorithms, theories and features to further improve the performance.</p> <p>Results</p> <p>In this study, we introduce a novel machine learning model hidden Markov support vector machine for protein binding site prediction. The model treats the protein binding site prediction as a sequential labelling task based on the maximum margin criterion. Common features derived from protein sequences and structures, including protein sequence profile and residue accessible surface area, are used to train hidden Markov support vector machine. When tested on six data sets, the method based on hidden Markov support vector machine shows better performance than some state-of-the-art methods, including artificial neural networks, support vector machines and conditional random field. Furthermore, its running time is several orders of magnitude shorter than that of the compared methods.</p> <p>Conclusion</p> <p>The improved prediction performance and computational efficiency of the method based on hidden Markov support vector machine can be attributed to the following three factors. Firstly, the relation between labels of neighbouring residues is useful for protein binding site prediction. Secondly, the kernel trick is very advantageous to this field. Thirdly, the complexity of the training step for hidden Markov support vector machine is linear with the number of training samples by using the cutting-plane algorithm.</p

Scoring docking conformations using predicted protein interfaces

BACKGROUND: Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a complex is especially useful for drug design, limitations of experimental techniques have restricted their practical use. Despite progress in docking predictions, there is still room for improvement. In this study, we contribute to this topic by proposing T-PioDock, a framework for detection of a native-like docked complex 3D structure. T-PioDock supports the identification of near-native conformations from 3D models that docking software produced by scoring those models using binding interfaces predicted by the interface predictor, Template based Protein Interface Prediction (T-PIP). RESULTS: First, exhaustive evaluation of interface predictors demonstrates that T-PIP, whose predictions are customised to target complexity, is a state-of-the-art method. Second, comparative study between T-PioDock and other state-of-the-art scoring methods establishes T-PioDock as the best performing approach. Moreover, there is good correlation between T-PioDock performance and quality of docking models, which suggests that progress in docking will lead to even better results at recognising near-native conformations. CONCLUSION: Accurate identification of near-native conformations remains a challenging task. Although availability of 3D complexes will benefit from template-based methods such as T-PioDock, we have identified specific limitations which need to be addressed. First, docking software are still not able to produce native like models for every target. Second, current interface predictors do not explicitly consider pairwise residue interactions between proteins and their interacting partners which leaves ambiguity when assessing quality of complex conformations

Učinak bakra na toksičnost i genotoksičnost kadmija u vodenoj leći (Lemna minor L.)

We investigated interactions between copper (in the concentrations of 2.5 μmol L-1 and 5 μmol L-1) and cadmium (5 μmol L-1) in common duckweed (Lemna minor L.) by exposing it to either metal or to their combinations for four or seven days. Their uptake increased with time, but it was lower in plants treated with combinations of metals than in plants treated with either metal given alone. In separate treatments, either metal increased malondialdehyde (MDA) level and catalase and peroxidase activity. Both induced DNA damage, but copper did it only after 7 days of treatment. On day 4, the combination of cadmium and 5 μmol L-1 copper additionally increased MDA as well as catalase and peroxidase activity. In contrast, on day 7, MDA dropped in plants treated with combinations of metals, and especially with 2.5 μmol L-1 copper plus cadmium. In these plants, catalase activity was higher than in copper treated plants. Peroxidase activity increased after treatment with cadmium and 2.5 μmol L-1 copper but decreased in plants treated with cadmium and 5 μmol L-1 copper. Compared to copper alone, combinations of metals enhanced DNA damage after 4 days of treatment but it dropped on day 7. In conclusion, either metal given alone was toxic/genotoxic and caused oxidative stress. On day 4 of combined treatment, the higher copper concentration was more toxic than either metal alone. In contrast, on day 7 of combined treatment, the lower copper concentration showed lower oxidative and DNA damage. These complex interactions can not be explained by simple antagonism and/or synergism. Further studies should go in that direction.U svrhu istraživanja interakcija između bakra kao esencijalnog elementa te kadmija kao neesencijalnog i toksičnog metala, vodenu leću Lemna minor L. uzgajali smo na podlogama s kadmijem (5 μmol L-1) odnosno s bakrom (2,5 μmol L-1 i 5 μmol L-1) te s njihovim kombinacijama. Unos metala u biljke povećavao se s trajanjem pokusa, a kod kombinacije metala u biljkama je izmjerena niža količina kadmija nego u onima uzgajanima samo na kadmiju. U biljkama tretiranim pojedinačnim metalom došlo je do povećanja sadržaja malondialdehida (MDA) te aktivnosti katalaze i peroksidaze u odnosu na kontrolne biljke. Također, primijećeno je oštećenje DNA iako kod bakra tek sedmog dana tretmana. Količina MDA i aktivnost obaju enzima dodatno se povećala na tretmanu kombinacijom kadmija i bakra (5 μmol L-1) nakon četvrtog dana pokusa, dok se količina MDA smanjila nakon sedmog dana kod kombinacije kadmija i 2,5 μmol L-1 bakra. U tim biljkama primijećena je i veća aktivnost katalaze, dok je aktivnost peroksidaze porasla na tretmanu kadmijem i 2,5 μmol L-1 bakrom, ali se smanjila na tretmanu kadmijem i 5 μmol L-1 bakrom. Oštećenje DNA koje je bilo veće kod kombinacije metala nakon četvrtog dana, osobito u usporedbi sa samim bakrom, smanjilo se nakon sedmog dana pokusa. Iz ovih rezultata može se zaključiti da su oba metala u istraživanim koncentracijama toksična i genotoksična za vodenu leću i da uzrokuju oksidacijski stres. Kadmij u kombinaciji s bakrom više koncentracije bio je toksičniji od pojedinačnih metala nakon četvrtog dana pokusa, dok su u biljaka tretiranih kombinacijom kadmija i bakra niže koncentracije toksični učinci bili manji. Budući da su primijećene interakcije vrlo kompleksne i ne uključuju samo antagonizam odnosno sinergizam potrebna su daljnja istraživanja

Paleogeographic evolution of the Southern Pannonian Basin: 40Ar/39Ar age constraints on the Miocene continental series of notthern Croatia

The Pannonian Basin, originating during the Early Miocene, is a large extensional basin incorporated between Alpine, Carpathian and Dinaride fold-thrust belts. Back-arc extensional tectonics triggered deposition of up to 500-m-thick continental fluvio-lacustrine deposits distributed in numerous sub-basins of the Southern Pannonian Basin. Extensive andesitic and dacitic volcanism accompanied the syn-rift deposition and caused a number of pyroclastic intercalations. Here, we analyze two volcanic ash layers located at the base and top of the continental series. The lowermost ash from Mt. Kalnik yielded an 40Ar/39Ar age of 18.07 ± 0.07 Ma. This indicates that the marine-continental transition in the Slovenia-Zagorje Basin, coinciding with the onset of rifting tectonics in the Southern Pannonian Basin, occurs roughly at the Eggenburgian/ Ottnangian boundary of the regional Paratethys time scale. This age proves the synchronicity of initial rifting in the Southern Pannonian Basin with the beginning of sedimentation in the Dinaride Lake System. Beside geodynamic evolution, the two regions also share a biotic evolutionary history: both belong to the same ecoregion, which we designate here as the Illyrian Bioprovince. The youngest volcanic ash level is sampled at the Glina and Karlovac sub-depressions, and both sites yield the same 40Ar/39Ar age of 15.91 ± 0.06 and 16.03 ± 0.06 Ma, respectively. This indicates that lacustrine sedimentation in the Southern Pannonian Basin continued at least until the earliest Badenian. The present results provide not only important bench marks on duration of initial synrift in the Pannonian Basin System, but also deliver substantial backbone data for paleogeographic reconstructions in Central and Southeastern Europe around the Early–Middle Miocene transition